Ed,
> On a practical side, I now have a misleading bond_rmsd value. The
> correct one can be calculated as described, but this may make geometry
> weight optimization cumbersome. Do I understand correctly that an
> alternative is to monitor Zbonds, with a rule that it should be around
> 1.0?
No
>> And more generally, shouldn't we not look at rmsd_bonds at all and
>> only use Zbonds instead (which is, I assume, an average bond length
>> deviation to the target value ratio?)
Sorry, I just realised that I misread what you wrote (that's what
comes of speed-reading!). What you said above is
On 10/14/10 11:22, Ed Pozharski wrote:
Again, definitions are a matter of choice
There is no "correct" definition of anything.
Definitions are a matter of community choice, not personal choice; i.e.
a matter of convention. If you come across a short squat animal with
split hooves rooting
Garib,
indeed - I tested 5.6.077 and the bond_rmsd is down to 0.006 as it
should. Thanks,
Ed.
On Thu, 2010-10-14 at 22:04 +0100, Garib N Murshudov wrote:
> Hi Ed
>
> refmac 5.6 should not have this problem. Yes, you are right. It should be
> considered as a bug.
> I think I have fixed it. C
As usual, the Omniscient Wikipedia does a pretty good job of giving the
standard mathematical definition of a "vector":
http://en.wikipedia.org/wiki/Vector_space#Definition
If the thing fulfills the axioms, it's a vector. Complex numbers do, as well
as scalars.
On Oct 15, 2010, at 8:56 AM,
Douglas,
The elements of a 'vector space' are not 'vectors' in the physical
sense.
The correct Wikipedia page is this one
http://en.wikipedia.org/wiki/Euclidean_vector
Ganesh
On Fri, 15 Oct 2010 11:20:04 -0400, Douglas Theobald
wrote:
> As usual, the Omniscient Wikipedia does a pretty goo
On Oct 15, 2010, at 11:37 AM, Ganesh Natrajan wrote:
> Douglas,
>
> The elements of a 'vector space' are not 'vectors' in the physical
> sense.
And there you make Ed's point -- some people are using the general vector
definition, others are using the more restricted Euclidean definition.
Th
> As usual, the Omniscient Wikipedia does a pretty good job of giving the
> standard mathematical definition of a "vector":
>
> http://en.wikipedia.org/wiki/Vector_space#Definition
>
> If the thing fulfills the axioms, it's a vector. Complex numbers do, as well
> as scalars.
It is a bit mo
Maybe this will shed insight into the problem:
What do you get when you cross a mosquito with a rock climber?
Nothing. You can't cross a vector and a scalar
Have a good weekend,
JPK
On Oct 15, 2010, at 12:14 PM, William G. Scott wrote:
>> As usual, the Omniscient Wikipedia does a pretty good job of giving the
>> standard mathematical definition of a "vector":
>>
>> http://en.wikipedia.org/wiki/Vector_space#Definition
>>
>> If the thing fulfills the axioms, it's a vector.
Oh dear, here we go again.
I know that there are people out there who have a hard time accepting
quantum mechanics, but yes, each "photon" really does interact with
EVERY ELECTRON IN THE CRYSTAL at once. Young's double-slit experiment
is the simplest form of diffraction, which he performed in
Thanks, Ian, this is excellent. It appears that depending on the
sequence the "ideal target rmsd" may vary from 0.018 for a poly-H to
0.024 for a poly-P. Except for some really short sequences, in PDB the
variation is generally between 0.021-0.022, indeed undetectable.
On Fri, 2010-10-15 at 10:2
Actually, people forget the 1/r term because it is gone by the end of
Chapter 6 of Woolfson.
Yes, it is true that, for the single "reference electron" the scattered
intensity falls off with the inverse square law of distance (r) and,
hence, the amplitude falls off with 1/r. However, the units
I couldn't resist:
What do you get when you cross an elephant with an orange?
Elephant.orange.sin(theta)
Frances
=
Bernstein + Sons
* * Information Systems Consultants
5 Brewster Lane, B
Any vector, whether in the 'mathematical' or 'physical' sense as
defined in Wikipedia, and which is defined on a 3D vector space
(Euclidean or otherwise - which I hope is what were talking about),
has by definition 3 elements (real or complex). This clearly excludes
all scalars (real or complex) wh
To upgrade the Refmac version that I am running from inside the CCP4i, I
did the following
mv $CCP4/bin/refmac5 $CCP4/bin/refmac5.5
cp refmacgfortran $CCP4/bin/refmac5.6
ln -s $CCP4/bin/refmac5.6 $CCP4/bin/refmac5
It seems to have worked fine. Is there more intelligent way of doing
this?
--
E
Our supplies of trimethyl lead acetate are running low. Does anybody
know of a chemical supplier that still makes it.
Matthew Vetting
>but yes, each "photon" really does interact with
EVERY ELECTRON IN THE CRYSTAL at once.
Take a crystal from the cave...10m long..perhaps not 'really'...
It is however helpful to think of a coherence volume
of the photon in which it interacts with every atom.
We had some discussions and estima
>but yes, each "photon" really does interact with
EVERY ELECTRON IN THE CRYSTAL at once.
Take a crystal from the cave...10m long..perhaps not 'really'...
It is however helpful to think of a coherence volume
of the photon in which it interacts with every atom.
We had some discussions and estim
>but yes, each "photon" really does interact with
EVERY ELECTRON IN THE CRYSTAL at once.
A minor point: the interaction is not really "at once," is it? The photon
does have to move through the crystal over a finite time.
JPK
Hi Matthew,
Try http://www.scbt.com/datasheet-233809-acetoxytrimethyllead-iv.html
Cheers,
Martin
On Oct 15, 2010, at 7:54 PM, matthew vetting wrote:
> Our supplies of trimethyl lead acetate are running low. Does anybody
> know of a chemical supplier that still makes it.
>
>
In temporary sense, the 'at once' I think really means this -
poof - photon gone - pop - photon comes out.
I am afraid one has to absolve oneself from the travelling
photon picture once a QM transition occurs.
br
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk]
Vectors are not only three-dimensional, nor only Euclidean -- vectors can be
defined for any number of arbitrary dimensions. Your initial comment referred
to complex numbers, for instance, which are 2D vectors (not 1-D). Obviously
scalars are not 3-vectors, they are 1-vectors. And contrary to
The photon moves through the crystal in finite time and most of the time
it keeps going without interacting with the crystal, i.e. no
diffraction. However, if diffraction occurs it is instantaneous, or at
least so fast as to consider it instantaneous. In some cases a
diffracted photon diffracts
On 10-10-15 10:37 AM, James Holton wrote:
...
In fact, anyone with a Pilatus detector (and a lot of extra beam
time) can verify the self-interference of photons in macromolecular
crystal diffraction. Since the source-to-detector distance of a
typical MX beamline is about 30 m, it takes 100
btw, buckyballs have measurable wave properties. i think they are trying virus
particles now.
On 10/15/10 12:38, Bart Hazes wrote:
> The photon moves through the crystal in finite time and most of the time
> it keeps going without interacting with the crystal, i.e. no
> diffraction. However, if diffraction occurs it is instantaneous, or at
> least so fast as to consider it instantaneous. In
Arndt, M.; O. Nairz, J. Voss-Andreae, C. Keller, G. van der Zouw, A.
Zeilinger (14 October 1999). "Wave-particle duality of C60". Nature 401:
680-682. doi:10.1038/44348.
They came up with 2.5 pm for the C60.
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Be
On 10-10-15 02:14 PM, Dale Tronrud wrote:
...
The photon both diffracts and doesn't diffract as it passes through
the crystal and it diffracts into all the directions that match the Bragg
condition. The wave function doesn't collapse to a single outcome until
the detector measures something
If I remember correctly, NaF forms octahedral crystals. Be sure to
check for salt crystals in your reservoir well.
ho
A couple of twinning-related questions.
I have a protein-DNA complex in P65. Protein binds DNA as a dimer, DNA
itself is not palindromic and has sticky ends located asymmetrically
with respect to the protein (dimer).
DNA contains a single fluoro-uracil which is flipped into the active
site. Thi
Dear colleagues,
I have a tartaric acid on a two fold axis with its two halves related
by the two fold. How do I refine this in Phenix?
Also I have a SO4 on a 3 fold with S and one O on tthe 3 fold. The
other 3 oxygens are related by the 3-fold. How do I refine this in
phenix? I can put S and
I try not to advertise SHELX too often on CCP4bb, but this is
just the sort of disorder problem that small molecule
crystallographers handle successfully and rather frequently
with SHELX. The use of 'free variables' for tying occupancies
together and restraining distances to be equal is something
On Fri, Oct 15, 2010 at 8:11 PM, Douglas Theobald
wrote:
> Vectors are not only three-dimensional, nor only Euclidean -- vectors can be
> defined for any number of arbitrary dimensions. Your initial comment
> referred to complex numbers, for instance, which are 2D vectors (not 1-D).
> Obvious
Hi Ed,
> To upgrade the Refmac version that I am running from inside the CCP4i, I
> did the following
>
> mv $CCP4/bin/refmac5 $CCP4/bin/refmac5.5
> cp refmacgfortran $CCP4/bin/refmac5.6
> ln -s $CCP4/bin/refmac5.6 $CCP4/bin/refmac5
>
> It seems to have worked fine. Is there more intelligent w
All the crystals I got for three different proteins in same condition looked
similar. I think crystal morphology may vary with the crystallizing conditions.
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